If you get something like "No such file or directory" instead of the list of files for the first ls command - unfortunately, Magento downloader registered a wrong path for the mentioned file. In that case the easiest way is to remove the entire extension manually.

Not only the only file but total extension , I have removed every file related to Extension manually by searching 'grep -i -n -r' but still it is in Connect manager. i have submitted two extensions to M-connect those are live , when i am trying to un install both by connect manager ".......:( “Check permissions”. Please Help
– Krishna ijjadaNov 20 '15 at 10:19

Actually, it's a bit tricky deal to remove a record from the Magento Connect configuration. The configuration is stored in /downloader/cache.cfg . You can try to decode it, remove the record and encode back like Alan mentioned here goo.gl/Qws1pj . Or you can try to sync all your extensions with Magento Connect in order to rebuild your cache.cfg file like it mentioned here goo.gl/d7aHXE . Anyway, if you have removed the extension manually - you may not bother with the 'chunk' in the cache.cfg, it should not cause issues for the store's functionality but might cost you many hours
– Yaroslav RogozaNov 20 '15 at 10:38

Great in-depth answer , but It is happening for every installation for every customer . Do i need to modify anything in my extensions ( Out of stock Noti, Category slider )?. In the same time i have tried to uninstall example extension by using Magento connect replies " Package deleted: Cache cleaned successfully".
– Krishna ijjadaNov 20 '15 at 11:14

First of all, try to check package.xml inside of your packed extension. There you will find XML tree of the extension's directories/files and their hashsums. You might find the broken path (...app/design/app/design/...) there.
– Yaroslav RogozaNov 20 '15 at 11:20